We may very well find out that the US security services were complicit in the Clinton arrangement. It would truly be absurd for a modern diplomat to be using insecure communications when things like (war, life, death) etc are the subject of the communiques.
Clearly the entire POTUS/administration infrastructure was sending her e-mails, so it seems to beggar belief that the system was not vetted by the secret service and the NSA.
On the other hand, the internal politics of mid-level burecrats in the state house are on a whole nother level of banality. The record keeping is certainly an issue, but its really an apples and banannas comparison.